8TKC: HIV-1 BG505DS-SOSIP.664 env trimer

cryo-EM structure of HIV-1 BG505DS-SOSIP.664 env trimer bound to DJ85-b.01 FAB. Determined by electron microscopy at 3.1 Å resolution. Released 28 Aug 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 20,064
Mol. weight: 378.49 kDa
Ligands: NAG
Released: 28 Aug 2024

Explore 8TKC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TKC contains 66 α-helices and 213 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	1
β-strand	45-47	3	2
β-strand	53-56	4	3
β-strand	67	1	4
β-strand	75-76	2	3
α-helix	77-78	2
β-strand	83-86	4	2
β-strand	91-94	4	5
α-helix	95-97	3
α-helix	99-115	17
β-strand	121	1	6
α-helix	123-125	3
β-strand	129-133	5	7
β-strand	138	1	8
β-strand	154-162	9	7
β-strand	169-177	9	7
β-strand	181-183	3	7
β-strand	190-193	4	7
α-helix	194-197	4
β-strand	202	1	6
β-strand	203	1	9
α-helix	204-205	2
β-strand	209	1	4
β-strand	215	1	10
β-strand	216-218	3	3
β-strand	223-228	6	2
β-strand	236-239	4	5
β-strand	242-245	4	2
β-strand	247	1	3
α-helix	248-250	3
β-strand	251	1	10
β-strand	261	1	11
β-strand	271-273	3	11
β-strand	284-298	15	11
β-strand	301	1	12
β-strand	304-312	7	13
β-strand	315-320	6	13
β-strand	323	1	12
β-strand	326	1	8
β-strand	330-334	5	11
α-helix	335-349	15
β-strand	358-361	4	11
α-helix	369-372	4
β-strand	374-378	5	14
β-strand	381-385	5	14
β-strand	393-395	3	11
β-strand	413-417	5	11
β-strand	418-421	4	14
β-strand	423-424	2	9
β-strand	434-435	2	9
α-helix	436-440	5
β-strand	443-456	14	11
β-strand	465-470	6	11
α-helix	476-480	5
β-strand	486-491	6	2
β-strand	495-499	5	1

Chain B: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	516-519	4	15
α-helix	524-526	3
α-helix	530-533	4
α-helix	537-542	6
α-helix	570-595	26
β-strand	603-609	7	1
α-helix	620-623	4
α-helix	628-634	7
α-helix	640-662	23

Chain C: 10 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	16
β-strand	45-47	3	17
β-strand	53-55	3	18
β-strand	56	1	19
β-strand	67	1	20
α-helix	75	1
β-strand	76	1	19
α-helix	77-78	2
β-strand	83-86	4	17
β-strand	91-94	4	21
α-helix	95-97	3
α-helix	99-115	17
β-strand	121	1	22
α-helix	123-125	3
β-strand	129-133	5	23
β-strand	138	1	24
β-strand	154-162	9	23
β-strand	169-177	9	23
β-strand	181-183	3	23
β-strand	190-193	4	23
β-strand	202	1	22
β-strand	203	1	25
β-strand	209	1	20
β-strand	215	1	26
β-strand	216-218	3	18
β-strand	223-228	6	17
β-strand	236-239	4	21
β-strand	242-245	4	17
β-strand	247	1	18
α-helix	248-250	3
β-strand	251	1	26
β-strand	261	1	27
β-strand	271-273	3	27
β-strand	284-298	15	27
β-strand	301	1	28
β-strand	304-312	7	29
β-strand	315-320	6	29
β-strand	323	1	28
β-strand	326	1	24
β-strand	329-334	6	27
α-helix	335-352	18
β-strand	358-361	4	27
α-helix	369-372	4
β-strand	374-378	5	27
β-strand	381-385	5	27
β-strand	393-395	3	27
β-strand	413-421	9	27
β-strand	423	1	25
β-strand	435	1	25
α-helix	436-440	5
β-strand	443-456	14	27
β-strand	465-470	6	27
α-helix	476-480	5
β-strand	486-491	6	17
β-strand	494-499	6	16

Chain D: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	517-519	3	30
α-helix	522-526	5
α-helix	530-533	4
α-helix	537-542	6
α-helix	570-595	26
β-strand	603-609	7	16
α-helix	619-621	3
α-helix	628-635	8
α-helix	640-662	23

Chain E: 12 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	31
β-strand	45-47	3	32
β-strand	53-55	3	33
β-strand	56	1	34
β-strand	67	1	35
α-helix	75	1
β-strand	76	1	34
α-helix	77-78	2
β-strand	83-86	4	32
β-strand	91-94	4	36
α-helix	95-97	3
α-helix	99-115	17
β-strand	121	1	37
α-helix	123-125	3
β-strand	129-133	5	38
β-strand	138	1	39
β-strand	154-162	9	38
β-strand	169-177	9	38
β-strand	181-183	3	38
β-strand	190-193	4	38
α-helix	194-197	4
β-strand	202	1	37
β-strand	203	1	40
α-helix	204-205	2
β-strand	209	1	35
β-strand	215	1	41
β-strand	216-218	3	33
β-strand	223-228	6	32
β-strand	236-239	4	36
β-strand	242-245	4	32
β-strand	247	1	33
α-helix	248-250	3
β-strand	251	1	41
β-strand	261	1	42
β-strand	271-273	3	42
β-strand	284-298	15	42
β-strand	301	1	43
β-strand	304-312	7	44
β-strand	315-320	6	44
β-strand	323	1	43
β-strand	326	1	39
β-strand	329-334	6	42
α-helix	335-349	15
β-strand	358-361	4	42
α-helix	369-372	4
β-strand	374-378	5	42
β-strand	381-385	5	42
β-strand	393-395	3	42
β-strand	413-421	9	42
β-strand	423-424	2	40
β-strand	434-435	2	40
α-helix	436-439	4
β-strand	443-457	15	42
β-strand	465-470	6	42
α-helix	476-480	5
β-strand	486-491	6	32
β-strand	494-499	6	31

Chain F: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	517-519	3	45
α-helix	522-526	5
α-helix	530-533	4
α-helix	537-541	5
α-helix	570-595	26
β-strand	603-609	7	31
α-helix	620-623	4
α-helix	628-634	7
α-helix	640-662	23

Chains G, I and K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	46
β-strand	11-13	3	47
β-strand	18-25	8	46
β-strand	34-39	7	15
β-strand	45-52	8	15
β-strand	57-59	3	15
β-strand	67-72	6	46
β-strand	77-82	6	46
α-helix	84-86	3
β-strand	88-99	12	15
β-strand	100J-103	5	15
β-strand	107-109	3	15
β-strand	110-112	3	47

Chain H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	48
β-strand	10-13	4	49
β-strand	19-25	7	48
β-strand	34-38	5	49
β-strand	44-49	6	49
β-strand	53-54	2	49
α-helix	55	1
β-strand	62-67	6	48
β-strand	70-75	6	48
α-helix	80-82	3
β-strand	84-89	6	49
α-helix	96	1
β-strand	97	1	15
β-strand	98	1	49
β-strand	102-106	5	49

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BG505 DS-SOSIP Surface protein gp120	A, C, E	protein	481	Human immunodeficiency virus 1	Q2N0S6
BG505 DS-SOSIP Transmembrane protein gp41	B, D, F	protein	153	Human immunodeficiency virus 1	Q2N0S5
DJ85-b.01 FAB heavy chain	G, I, K	protein	240	Homo sapiens
DJ85-b.01 FAB light chain	H, J, L	protein	214	Homo sapiens

Sequence of entity 1 (A, C, E), FASTA

>8TKC_1 BG505 DS-SOSIP Surface protein gp120 (chains A, C, E)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 2 (B, D, F), FASTA

>8TKC_2 BG505 DS-SOSIP Transmembrane protein gp41 (chains B, D, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (G, I, K), FASTA

>8TKC_3 DJ85-b.01 FAB HEAVY CHAIN (chains G, I, K)
QVQLQESGPGLVKASETLSLTCAVSGASVSGNYYWNWIRQSPGKELEWIGNIHGNSGTTT
YNPSLESRVTISTDTSKNQFSLKLTSVTGADTATYFCATQFKKYWGLSVSSPFSFSDSWG
QGVLVSVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGLEVLFQ

Sequence of entity 4 (H, J, L), FASTA

>8TKC_4 DJ85-b.01 FAB LIGHT CHAIN (chains H, J, L)
DIQMTQSPRSLSASVGDRVTITCRASQDISPDLNWYQQKPGGPLKLLIYDASNLQGGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCLQYNGYPWTFGQGTKVDHKRTVAAPSVFIFPP
SEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSLSSTLT
LSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15

Primary citation

Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques. Wang, H., Cheng, C., Dal Santo, J.L. et al. Cell (2024) 187:7214-7231.e23. DOI 10.1016/j.cell.2024.10.003 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S6), best resolution first:

8TOX 2.3 Å, Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
6MTJ 2.34 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6W03 2.4 Å, Crystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with…
6MTN 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6UDJ 2.5 Å, HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074
8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6MU7 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6MU6 2.55 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6NNJ 2.6 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in…
8EUV 2.6 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB
8T4K 2.6 Å, MD64 N332-GT5 sosip
8EUU 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB

Browse structure collections

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